ok so with the master cyl on the booster the pedal stops about 2 inchs from the floor and makes a click/clunk sound. The brakes are not bled. removed the master cyl from the booster and the pedal goes right to the floor with no effort and does not clunk.

same thing happend with the old master cyl sooo.. that must not be the problem then. but the brake booster is fine without the master cyl so i cant see it being a problem ethier. i cant imagine air in the brakes doing this. it is like the booster has pushed the masster cyl as far as it can go.